I. Welcome to PLATCOM !

PCDB GenomePlot OperonViz
MCGS FuzFinder MetaPath
BAG Clustering mgALIGN GAME
COMPAM ComPath iGibbs
EGGS CLASSEQ


PLATCOM is an integrated system for the comparative analysis of multiple genomes. It is designed in a modular way, so that multiple tools and databases can be integrated freely and the whole system can grow easily. The PLATCOM system is built on internal databases, which consist of GenBank, Swiss-Prot, COG, KEGG, and Pairwise Comparison Database (PCDB). PCDB is a derived database from GenBank built by performing pairwise comparison of protein-to-protein and whole genome-to-whole genome sequences with FASTA and BLASTZ respectively. Currently it contains 48,205 entries of unduplicated protein-to-protein and whole genome-to-whole genome pairwise comparison matches. PCDB is designed to incorporate newer genomes automatically, so that PLATCOM evolves as new genomes become available. Over these databases, a suite of genome analysis applications are provided.

II. System Integration via Defined Data Types

The philosophy in designing the PLATCOM system aims to implement the functional composition of basic analysis modules, which gives the system extensibility and provides users with a huge amount of flexibility in designing experiments. Owing to its modular design, each genome analysis tool can be functionally connected with other component tools and command-line tools with ease. GenomePlot, OperonViz, FuzFinder, MetaPath, muti-genome alignment and sequence clustering tools are provided as a suite of genomic data mining tools and more component tools will be added in the near future. System modules can be integrated as long as the co-domain of a module is of the same data type as the domain of another module. In the Fig 1, solid lines with a data type label show how modules are integrated with a genome data type (i.e. DT) denoted by the label. Dotted lines show that results from each module can be saved in the user event management system. Four data types are shown in Fig 1 : G = genome set DT, Cs = gene cluster DT, Ss = gene set DT, and T = table DT


Fig 1. The Workflow within PLACOM system: (G = genome set DT, Cs = gene cluster DT, Ss = gene set DT, T = table DT)

III. Publications

Year Title Authors Publisher Comment
2006 BAG: A Graph Theoretic Sequence Clustering Algorithm, 1(2), pp 178-200 un Kim and Jason Lee International Journal of Data Mining and Bioinformatics Research article
2006 Genome Data Type: a Vehicle to Deliver a Genome Comparison System on the Web Kwangmin Choi, Amit Saple, and Sun Kim IEEE ICDM 2006 Workshop on Data Mining in Bioinformatics (Dec. 2006), Hong Jong, China System design
2006 iGibbs: Improved Gibbs Motif Sampler for Proteins by Sequence Clustering and Iterative Pattern Refinement Sun Kim, Zhiping Wang, and Mehmet Dalkilic Proteins: Structure, Function, and Bioinformatics Research Article
2006 ARCS: An Aggregated Related Column Scoring Scheme for Aligned Sequences Guangyu Chen, Jeong-Hyeon Choi, Bin Song, John Chmura, GQ Zhang, Anthony K.H. Tung, Jaewoo Kang, Sun Kim, and Jiong Yang Bioinformatics Research Article (in press)
2006 Comparative Genome Annotation Systems Kwangmin Choi and Sun Kim Advanced Data Mining Technologies in Bioinformatics. edited by Hui-Huang Hsu, Idea Group, Inc. Book Chapter
2006 BAG: A Graph Theoretic Sequence Clustering Algorithm Sun Kim and Jason Lee International Journal of Data Mining and Bioinformatics (IJDMB) Research Article (in press)
2005 A Hybrid Gene Team Model and Its Application to Genome Analysis Sun Kim, Jeong-Hyeon Choi, Amit Saple and Jiong Yang Journal of Bioinformatics & Computational Biology, 2005 Nov. Research Article (accepted)
2005 Gene Teams with Relaxed Proximity Constraint Sun Kim, Jeong-Hyeon Choi, and Jiong Yang IEEE Computational Systems Bioinformatics (CSB'05), pp 44-55, August 2005, San Francisco, 2005 Dec 16 Conference Paper, Suppliment
2005 COMPAM :Visualization of Combining Pairwise alignment for Multiple Genomes DoHoon Lee, Jeong-Hyeon Choi, Mehmet Dalkilic, and Sun Kim Bioinformatics, 2005 Dec 16 Application Note
2005 PLATCOM: a Platform for Computational Comparative Genomics on the Web Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim CSB Workshops 2005: 27-30 Postition Paper
2005 PLATCOM: Current Status and Plan for the Next Stages Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, and Sun Kim Data Integration in the Life Sciences 2005: No. 3615 in Lecture Notes in Bioinformatics, pp 300-304, June, 2005, San Diego Lecture Note
2005 PLATCOM: A Platform for Computational Comparative Genomics Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, and Sun Kim Bioinformatics 2005: 15;21(10):2514-6 Application Note
2005 A Simple and Efficient Alignment Method for Microbial Whole Genomes Using Maximal Exact Match Filtering Choi, J.-H., Cho, H.-G., and Kim, S. Computational Biology and Chemistry 2005: 29(3), 244-253 Research Paper
2005 A Data Management Architecture for Computational Biology Ma, Y., Bramley, R., and Kim, S. Indiana University Computer Science Technical Report 607 Technocal Report
2004 Multiple Genome Alignment by Clustering Pairwise Matches Jeong-Hyeon Choi, Kwangmin Choi, Hwan-Gue Cho, and Sun Kim Proceedings of the 2nd RECOMB Comparative Genomics Satellite Workshop, Lecture Notes in Bioinformatics, Bertinoro, Italy, 3388 (2005). Springer-Verlag, Berlin Lecture Note
2003 Graph theoretic sequence clustering algorithms and their applications to genome comparison Sun Kim Chapter 4 in Computational Biology and Genome Informatics, World Scientific Book Chapter

IV. Acknowledgements

Thie project is funded by NSF CAREER Award DBI-0237901 INGEN (Indiana Genomics Initiatives), and AVIDD (Analysis and Visualization of Instrument-Driven Data) Linux cluster.

PLATCOM is accessible at http://platcom.informatics.indiana.edu/platcom.


Last Updated on July 7, 2007